DNA barcoding of Pedicularis L. (Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus
DNA barcoding of Pedicularis L. (Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus
复制标题
DOI：
10.1111/j.1759-6831.2011.00154.x
复制
发表时间：
2011-09
影响因子：
3.7
通讯作者：
Wen-bin Yu;Pan‐Hui Huang;R. Ree;Min-Lu Liu;De‐Zhu Li;Hong Wang
中科院分区：
文献类型：
--
作者：
Wen-bin Yu;Pan‐Hui Huang;R. Ree;Min-Lu Liu;De‐Zhu Li;Hong Wang
摘要 DNA 条形码的应用之一是基于短且标准化的 DNA 区域序列的物种识别。在植物中，各种单独或组合的 DNA 区域已经被提出并进行了研究，但关于通用植物条形码的共识仍然难以实现。在本研究中，我们测试了四个候选条形码区域（rbcL、matK、trnH-psbA 和内转录间隔区 (ITS)）作为 DNA 条形码用于区分大型半寄生马先蒿属（列当科）物种的效用。 rbcL、trnH-psbA 和 ITS 使用单引物对即可成功扩增和测序，而 matK 则需要两个引物对。序列分歧的模式通常表现出“条形码差距”，即分别代表物种内和物种间遗传多样性的成对距离的双峰频率分布。考虑到引物的通用性、扩增和测序的简易性以及区分物种的性能，我们发现马先蒿最有效的单区域条形码是ITS，最有效的双区域条形码是rbcL + ITS。两者都区分了 88 个物种中的至少 78%，并正确识别了样本中至少 89% 的序列，并且可以有效地将未识别的样本归入已知物种组中。我们的研究结果表明，DNA 条形码有潜力帮助马先蒿（一个物种丰富的国际化分支，急需修订）的分类学研究，以及其多样性中心（中国横断山脉地区）的生态研究。
Abstract One application of DNA barcoding is species identification based on sequences of a short and standardized DNA region. In plants, various DNA regions, alone or in combination, have been proposed and investigated, but consensus on a universal plant barcode remains elusive. In this study, we tested the utility of four candidate barcoding regions (rbcL, matK, trnH‐psbA, and internal transcribed spacer (ITS)) as DNA barcodes for discriminating species in a large and hemiparasitic genus Pedicularis (Orobanchaceae). Amplification and sequencing was successful using single primer pairs for rbcL, trnH‐psbA, and ITS, whereas two primer pairs were required for matK. Patterns of sequence divergence commonly showed a “barcoding gap”, that is, a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species, respectively. Considering primer universality, ease of amplification and sequencing, and performance in discriminating species, we found the most effective single‐region barcode for Pedicularis to be ITS, and the most effective two‐region barcode to be rbcL + ITS. Both discriminated at least 78% of the 88 species and correctly identified at least 89% of the sequences in our sample, and were effective in placing unidentified samples in known species groups. Our results suggest that DNA barcoding has the potential to aid taxonomic research in Pedicularis, a species‐rich cosmopolitan clade much in need of revision, as well as ecological studies in its center of diversity, the Hengduan Mountains region of China.